|
| Status |
Public on Jul 24, 2023 |
| Title |
endothelial_ATACseq_1dpa_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Heart
|
| Organism |
Danio rerio |
| Characteristics |
tissue: Heart
cell type: endothelial cells
genotype: Tg(fli1:EGFP)
treatment: 1 day post vetricular apex amputation
|
| Treatment protocol |
Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult fish between 4~12 month old were used in this study.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Heart ventricular resections are performed on adult Tg(fli1:EGFP) zebrafish. Hearts were collected at 1 dpa and 3dpa. Uninjured zebrafish hearts were used as control.
Hearts are dissociated dissociated using Liberase DH (Roche) and EGFP+ cells were isolated by FACS. 100,000 cells/nuclei were used for library preparation.
ATAC library preparation was performed as described in (Buenrostro et al., 2013).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
ATAC-Seq reads were trimmed by Trim Galore (0.4.1, with -q 15) and then mapped with bowtie2(2.2.5, with parameters --very-sensitive) to zebrafish genome (danRer10).
The mapped reads were filtered by MAPQ greater than 30 by samtools (v 1.5) and Bigwig files were generated by kentUtils.
Supplementary files format and content: danRer10
Supplementary files format and content: bigwig file coverted from coverage output by macs2
|
| |
|
| Submission date |
Aug 17, 2022 |
| Last update date |
Jul 24, 2023 |
| Contact name |
jianhong ou |
| E-mail(s) |
jou@morgridge.org
|
| Phone |
5084102796
|
| Organization name |
Morgridge institute for research
|
| Lab |
Regeneromics
|
| Street address |
330 N Orchard Street
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53715 |
| Country |
USA |
| |
|
| Platform ID |
GPL14875 |
| Series (1) |
| GSE211424 |
An injury responsive enhancer promotes heart regeneration in zebrafish |
|
| Relations |
| BioSample |
SAMN30360574 |
| SRA |
SRX17115066 |
